Both deleterious (pathogenic) and beneficial (mycorrhizal) fungi inhabit plant roots with strong impact on plant growth and health. Various methods have been used to quantify these fungi, such as indirect measurements of plant parameters, disease index, staining techniques and serological/genetic/biochemical markers. The objective of this work is to evaluate the possibility of using signature fatty acids to quantify root-inhabiting fungi in planta and in soil. Different fatty acid-based methods can be used to quantify fungi. Phospholid fatty acids (PLFA) can be used for biomass estimation and neutral lipid fatty acids (NLFA) for estimation of fungal energy reserves and the NLFA/PLFA ratio can give information on the physiological status of the fungus. It is quite laborious to make PLFA and NLFA analyses; so whole cell fatty acid (WCFA) analyses, which are much faster, can be used as a faster alternative to give information of root infection intensity.
Signature fatty acids have been used to quantify arbuscular mycorrhizal fungi (16:1ω5) and the pea root pathogen Aphanomyces euteiches (14:1ω9). Recently, we have further used arachadonic acid (20:4) to estimate root infection intensity of the plasmodiophorids Plasmodiophora brassica, causing club root in cabbage and Spongospora subterranea, the vector of mop top potato virus. Specificity of the various signature fatty acids of root-inhabiting fungi are discussed in relation to quantifying these fungi in both controlled greenhouse pot experiments and in the field. Furthermore, the possibility of using signature fatty acids to estimate soil inoculum potential of root-inhabiting fungi are discussed
